poseidon-framework / minotaur-recipes Goto Github PK

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Need to add documetation

Which package needs changes?

Package name: 2021_PattersonNature

Check for upcoming changes

I confirm there are no changes already suggested for this package that address
my issue in:

• Open Pull Requests
• Open Issues

What needs changing, and why?

The SSF for the package does not end in a new line, which skipped some of the data when processing.

(optional) What are the changes you'd like?

Add an new line at the SSF EOF, and recreate recipe.

(optional) How did you realise something needs updating?

The eager TSV was missing the last entry.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1126/sciadv.abd6535
• Project accession number:
  PRJEB40698

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

NOTE: This package was moved over from the poseidon-eager repo (see here). This issue is just for tracking of progress.

Currently, CaptureType profiles allow users to specify the processing that should be done on the data. However, there is a disctinction between the snpSet of a package and the Capture_Type of raw data, that is not exactly handled properly currently.

The current CaptureType profiles should perhaps be renamed to SnpSet profiles, as they govern which SNPs to genotype on and not really if the data is capture or not.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1016/j.cub.2022.11.036
• Project accession number:
  PRJEB57974

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Yes I'm working on this.

Which package needs changes?

Package name: 2020_Margaryan_Viking <- Replace the package name here with
the name of the relevant package.

Check for upcoming changes

I confirm there are no changes already suggested for this package that address
my issue in:

• Open Pull Requests
• Open Issues

What needs changing, and why?

Date formatting in SSF is not in YYYY-MM-DD format.

(optional) What are the changes you'd like?

(optional) How did you realise something needs updating?

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1073/pnas.2406734121 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB70768 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: doi:10.15184/aqy.2022.79 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB50901 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: http://dx.doi.org/10.1038/s41586-022-05247-2 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB54899 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Only people with write access can assign a person to issues. We might want to allow users to assign/unassign themselves from issues, which would then require delphis-bot to do so.

Which package needs changes?

Package name: 2021_CarlhoffNature <- Replace the package name here with
the name of the relevant package.

Check for upcoming changes

I confirm there are no changes already suggested for this package that address
my issue in:

• Open Pull Requests
• Open Issues

What needs changing, and why?

Removal of unnecessary subgroupings of TF/SG data into separate poseidon_Ids.

(optional) What are the changes you'd like?

(optional) How did you realise something needs updating?

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1016/j.cell.2023.10.018
• Project accession number: PRJEB66422

Will you work on this?

Yes, I have the SSF file ready.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1038/s41467-022-29158-y <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB49391 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1016/ j.isci.2023.108215 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB60362 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Currently, users do not have the right permissions to add a label to their PR, which is required for delphis to work.

I should either create a bot command for adding the label on request (perhaps a way to enforce SSF formatting passes checks?), or remove the label requirement altogether.

Which package needs changes?

Package name: 2020_Margaryan_Viking

Check for upcoming changes

I confirm there are no changes already suggested for this package that address
my issue in:

• Open Pull Requests
• Open Issues

What needs changing, and why?

The SSF for the package does not end in a new line, which skipped some of the data when processing.

(optional) What are the changes you'd like?

Add an new line at the SSF EOF, and recreate recipe.

(optional) How did you realise something needs updating?

The eager TSV was missing the last entry.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1126/science.add6142 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB51440 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this? nope, sorry!

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1016/j.isci.2022.104094
• Project accession number:
  PRJEB50940

Will you work on this?

Yes :)

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1016/j.cell.2022.11.024
• Project accession number: PRJEB57364

Will you work on this?

Yes

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1126/sciadv.adg3377 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB62808 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1038/s41559-023-02114-9 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  [[PRJEB51863][(https://www.ebi.ac.uk/ena/data/view/PRJEB51863)] <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1073/pnas.2005965117 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB37726 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.